accucor (version 0.3.1)

natural_abundance_correction: Natural Abundance correction for mass spectrometry data

Description

natural_abundance_correction returns the corrected and normalized intensities of isotopically labeled mass spectrometry data. It was designed to work with input data from El-MAVEN and MAVEN software.

Usage

natural_abundance_correction(
  data,
  sheet = NULL,
  compound_database = NULL,
  output_base = NULL,
  output_filetype = "xlsx",
  columns_to_skip = NULL,
  resolution,
  resolution_defined_at = 200,
  purity = NULL,
  report_pool_size_before_df = FALSE,
  path = NULL
)

Value

Named list of matrices: 'Corrected', 'Normalized', 'PoolBeforeDF', and 'PoolAfterDF'.

Arguments

data

Path to input data file (xlsx, xls, csv, txt, or tsv) OR dataframe. If dataframe is specified, specify output_base to output files automatically written.

sheet

Name of sheet in xlsx file with columns 'compound', 'formula', 'isotopelabel', and one column per sample. Defaults to the first sheet.

compound_database

Path to compound database in csv format. Only used for classic MAVEN style input when formula is not specified.

output_base

Path to basename of output file, default is the basename of the input path. `_corrected` will be appended. If `FALSE` then no output file is written.

output_filetype

Filetype of the output file, one of: 'xls', xlsx', 'csv', or 'tsv'. The default is 'xlsx'.

columns_to_skip

Specify column heading to skip. All other columns not named 'compound', 'formula', and 'isotopelabel' will be assumed to be sample names.

resolution

For Exactive, the resolution is 100000, defined at Mw 200

resolution_defined_at

Mw at which the resolution is defined, default 200 Mw

purity

Isotope purity, default: Carbon 0.99; Deuterium 0.98; Nitrogen 0.99

report_pool_size_before_df

Report PoolSizeBeforeDF, default = FALSE

path

Deprecated. Specify path to input data file (alias for `data`).

Details

C13, H2, and N15 isotopes are supported. The isotopes are detected from the isotopeLabel column of the input file. The expected label text is C13-label-#. D-label-#. or N15-label-#. Parent (unlabeled) compounds are specified by C12 PARENT.

Examples

if (FALSE) {
natural_abundance_correction("inst/extdata/C_Sample_Input_Simple.xlsx",
  Resolution = 100000, ResDefAt = 200
)
}